google colab python environment issues #145
Description
batchDownload.ipynbdoes not work out of box currently
Input:
!pip install -q condacolab
import condacolab
condacolab.install()
!pip install python-decouple
!pip install maskpass==0.3.6
!pip install requests
!conda install -c opensim-org opensim=4.4.1=py310np121
Output:
Solving environment: | warning libmamba Added empty dependency for problem type SOLVER_RULE_UPDATfailed
LibMambaUnsatisfiableError: Encountered problems while solving:
- package opensim-4.4.1-py310np121 requires python 3.10.*, but none of the providers can be installed
Could not solve for environment specs
The following packages are incompatible
├─ opensim ==4.4.1 py310np121 is installable and it requires
│ └─ python 3.10.* , which can be installed;
└─ pin-2 is not installable because it requires
└─ python 3.11** , which conflicts with any installable versions previously reported.
Input:
!pip install -q condacolab
import condacolab
condacolab.install()
!conda install -c opensim-org opensim
!git clone https://github.com/stanfordnmbl/opencap-processing.git
%cd /content/opencap-processing
!python3 -m pip install -r requirements.txt
import os
import sys
sys.path.append("..")
import numpy as np
import matplotlib.pyplot as plt
import utilsKinematics
from utils import download_kinematics
Errors:
A module that was compiled using NumPy 1.x cannot be run in
NumPy 2.0.2 as it may crash. To support both 1.x and 2.x
versions of NumPy, modules must be compiled with NumPy 2.0.
Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.
If you are a user of the module, the easiest solution will be to
downgrade to 'numpy<2' or try to upgrade the affected module.
We expect that some modules will need time to support NumPy 2.
Traceback (most recent call last): File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/usr/local/lib/python3.11/dist-packages/colab_kernel_launcher.py", line 37, in <module>
ColabKernelApp.launch_instance()
File "/usr/local/lib/python3.11/dist-packages/traitlets/config/application.py", line 992, in launch_instance
app.start()
File "/usr/local/lib/python3.11/dist-packages/ipykernel/kernelapp.py", line 712, in start
self.io_loop.start()
File "/usr/local/lib/python3.11/dist-packages/tornado/platform/asyncio.py", line 205, in start
self.asyncio_loop.run_forever()
File "/usr/lib/python3.11/asyncio/base_events.py", line 608, in run_forever
self._run_once()
File "/usr/lib/python3.11/asyncio/base_events.py", line 1936, in _run_once
handle._run()
File "/usr/lib/python3.11/asyncio/events.py", line 84, in _run
self._context.run(self._callback, *self._args)
File "/usr/local/lib/python3.11/dist-packages/ipykernel/kernelbase.py", line 510, in dispatch_queue
await self.process_one()
File "/usr/local/lib/python3.11/dist-packages/ipykernel/kernelbase.py", line 499, in process_one
await dispatch(*args)
File "/usr/local/lib/python3.11/dist-packages/ipykernel/kernelbase.py", line 406, in dispatch_shell
await result
File "/usr/local/lib/python3.11/dist-packages/ipykernel/kernelbase.py", line 730, in execute_request
reply_content = await reply_content
File "/usr/local/lib/python3.11/dist-packages/ipykernel/ipkernel.py", line 383, in do_execute
res = shell.run_cell(
File "/usr/local/lib/python3.11/dist-packages/ipykernel/zmqshell.py", line 528, in run_cell
return super().run_cell(*args, **kwargs)
File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 2975, in run_cell
result = self._run_cell(
File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 3030, in _run_cell
return runner(coro)
File "/usr/local/lib/python3.11/dist-packages/IPython/core/async_helpers.py", line 78, in _pseudo_sync_runner
coro.send(None)
File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 3257, in run_cell_async
has_raised = await self.run_ast_nodes(code_ast.body, cell_name,
File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 3473, in run_ast_nodes
if (await self.run_code(code, result, async_=asy)):
File "/usr/local/lib/python3.11/dist-packages/IPython/core/interactiveshell.py", line 3553, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-3-297b6a014f0a>", line 6, in <cell line: 0>
import utilsKinematics
File "/content/opencap-processing/utilsKinematics.py", line 22, in <module>
import opensim
File "/usr/local/lib/python3.11/site-packages/opensim/__init__.py", line 18, in <module>
from .simbody import *
File "/usr/local/lib/python3.11/site-packages/opensim/simbody.py", line 10, in <module>
from . import _simbody
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
AttributeError: _ARRAY_API not found
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-3-297b6a014f0a> in <cell line: 0>()
4 import numpy as np
5 import matplotlib.pyplot as plt
----> 6 import utilsKinematics
7 from utils import download_kinematics
2 frames
/usr/local/lib/python3.11/site-packages/opensim/simbody.py in <module>
8 # Import the low-level C/C++ module
9 if __package__ or "." in __name__:
---> 10 from . import _simbody
11 else:
12 import _simbody
ImportError: numpy.core.multiarray failed to import
---------------------------------------------------------------------------
NOTE: If your import is failing due to a missing package, you can
manually install dependencies using either !pip or !apt.
To view examples of installing some common dependencies, click the
"Open Examples" button below.
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